The Biasing Effect of Compositional Heterogeneity on Phylogenetic Estimates May be Underestimated

Jermiin, Lars S.; Ho, Simon Y. W.; Ababneh, Faisal; Robinson, John; Larkum, Anthony W. D.

doi:10.1080/10635150490468648

Cited by 240 publications

(182 citation statements)

References 51 publications

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“…The average GC content of the sequences was 0.45, and a 2 test at the 5% level of signiWcance for diVerences in base frequencies showed that there was no base compositional heterogeneity among sequences, which is known to adversely aVect phylogenetic inference (Jermiin et al, 2004).…”

Section: Resultsmentioning

confidence: 99%

Uplift of the Tibetan plateau: Evidence from divergence times of glyptosternoid catfishes

Peng

Zhang

et al. 2006

Molecular Phylogenetics and Evolution

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102

111

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Section: Resultsmentioning

confidence: 99%

Uplift of the Tibetan plateau: Evidence from divergence times of glyptosternoid catfishes

Peng

Zhang

et al. 2006

Molecular Phylogenetics and Evolution

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102

111

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“…This is a challenge because genomes of the ecologically distinct SAR11 and Rickettsiales lineages consistently exhibit low G þ C content whereas most members of the remaining alphaproteobacterial lineages contain G þ C-rich genomes. Such variability in nucleotide ratios frequently results in a clustering pattern influenced by compositional similarity rather than biological relatedness in phylogenomic reconstruction SAR11 evolutionary origin H Luo (Galtier and Gouy, 1995;Jermiin et al, 2004;Collins et al, 2005;Cox et al, 2008;Foster et al, 2009;Sheffield et al, 2009;Nesnidal et al, 2010;Guy et al, 2014). Here, the evolutionary position of the SAR11 clade was shown to be better resolved in two ways, either by applying a standard phylogenetic program (for example, RAxML) to a least biased data set, or by applying a compositionheterogeneous model to a data set that contains bias.…”

Section: Discussionmentioning

confidence: 99%

Evolutionary origin of a streamlined marine bacterioplankton lineage

Luo

2014

The ISME Journal

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Planktonic bacterial lineages with streamlined genomes are prevalent in the ocean. The base composition of their DNA is often highly biased towards low G þ C content, a possible source of systematic error in phylogenetic reconstruction. A total of 228 orthologous protein families were sampled that are shared among major lineages of Alphaproteobacteria, including the marine freeliving SAR11 clade and the obligate endosymbiotic Rickettsiales. These two ecologically distinct lineages share genome sizes of o1.5 Mbp and genomic G þ C content of o30%. Statistical analyses showed that only 28 protein families are composition-homogeneous, whereas the other 200 families significantly violate the composition-homogeneous assumption included in most phylogenetic methods. RAxML analysis based on the concatenation of 24 ribosomal proteins that fall into the heterogeneous protein category clustered the SAR11 and Rickettsiales lineages at the base of the Alphaproteobacteria tree, whereas that based on the concatenation of 28 homogeneous proteins (including 19 ribosomal proteins) disassociated the lineages and placed SAR11 at the base of the non-endosymbiotic lineages. When the two data sets were concatenated, only a model that accounted for compositional bias yielded a tree identical to the tree built with compositionhomogeneous proteins. Ancestral genome analysis suggests that the first evolved SAR11 cell had a small genome streamlined from its ancestor by a factor of two and coinciding with an ecological transition, followed by further gradual streamlining towards the extant SAR11 populations.

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“…The alignment of the ITS1-5.8S-ITS2 region sequences from the two bucephalids and the outgroup resulted in a total of 1,271 characters, including gaps. The average GC content of the sequences was 0.53, and a χ 2 test at the 5% level of significance for differences in base frequencies showed that there was no base compositional heterogeneity among sequences (χ 2 =5.05, df=114, P= 1.00), which is known to adversely affect phylogenetic inference (Jermiin et al 2004). Based on the alignment of the ITS1-5.8S-ITS2 region sequences from the two bucephalids, there were 1,145 character sites in the matrix, with 153 variable sites and 62 phylogeny-informative sites.…”

Section: Sequence Variationsmentioning

confidence: 99%

Utility of ITS1–5.8S–ITS2 sequences for species discrimination and phylogenetic inference of two closely related bucephalid digeneans (Digenea: Bucephalidae): Dollfustrema vaneyi and Dollfustrema hefeiensis

et al. 2007

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The complete internal transcribed spacer 1 (ITS1), 5.8S ribosomal DNA, and ITS2 region of the ribosomal DNA from 60 specimens belonging to two closely related bucephalid digeneans (Dollfustrema vaneyi and Dollfustrema hefeiensis) from different localities, hosts, and microhabitat sites were cloned to examine the level of sequence variation and the taxonomic levels to show utility in species identification and phylogeny estimation. Our data show that these molecular markers can help to discriminate the two species, which are morphologically very close and difficult to separate by classical methods. We found 21 haplotypes defined by 44 polymorphic positions in 38 individuals of D. vaneyi, and 16 haplotypes defined by 43 polymorphic positions in 22 individuals of D. hefeiensis. There is no shared haplotypes between the two species. Haplotype rather than nucleotide diversity is similar between the two species. Phylogenetic analyses reveal two robustly supported clades, one corresponding to D. vaneyi and the other corresponding to D. hefeiensis. However, the population structures between the two species seem to be incongruent and show no geographic and host-specific structure among them, further indicating that the two species may have had a more complex evolutionary history than expected.

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The Biasing Effect of Compositional Heterogeneity on Phylogenetic Estimates May be Underestimated

Cited by 240 publications

References 51 publications

Uplift of the Tibetan plateau: Evidence from divergence times of glyptosternoid catfishes

Uplift of the Tibetan plateau: Evidence from divergence times of glyptosternoid catfishes

Evolutionary origin of a streamlined marine bacterioplankton lineage

Utility of ITS1–5.8S–ITS2 sequences for species discrimination and phylogenetic inference of two closely related bucephalid digeneans (Digenea: Bucephalidae): Dollfustrema vaneyi and Dollfustrema hefeiensis

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